rs5906883

Variant names:

• chrX-43667695-A-C
• rs5906883
• NM_000240.4:c.73+11281A>C

Your query was ambiguous. Multiple possible variants found:

• chrX-43667695-A-C
• chrX-43667695-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000240.4(MAOA):​c.73+11281A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.60 (15007 hom., 18965 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 9 publications found

Genes affected

MAOA (HGNC:6833): (monoamine oxidase A) This gene is one of two neighboring gene family members that encode mitochondrial enzymes which catalyze the oxidative deamination of amines, such as dopamine, norepinephrine, and serotonin. Mutation of this gene results in Brunner syndrome. This gene has also been associated with a variety of other psychiatric disorders, including antisocial behavior. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Jul 2012]

MAOA Gene-Disease associations (from GenCC):

• Brunner syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAOA	NM_000240.4	c.73+11281A>C		intron_variant	Intron 1 of 14	ENST00000338702.4	NP_000231.1
MAOA	NM_001270458.2	c.-327+9726A>C		intron_variant	Intron 2 of 15		NP_001257387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAOA	ENST00000338702.4	c.73+11281A>C		intron_variant	Intron 1 of 14	1	NM_000240.4	ENSP00000340684.3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 66295 AN: 109951 Hom.: 15014 Cov.: 22

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.695

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.615

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.603 AC: 66302 AN: 110005 Hom.: 15007 Cov.: 22 AF XY: 0.587 AC XY: 18965 AN XY: 32317

African (AFR) AF: 0.446 AC: 13515 AN: 30288

American (AMR) AF: 0.666 AC: 6804 AN: 10217

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 1782 AN: 2623

East Asian (EAS) AF: 0.418 AC: 1454 AN: 3478

South Asian (SAS) AF: 0.376 AC: 991 AN: 2633

European-Finnish (FIN) AF: 0.555 AC: 3183 AN: 5730

Middle Eastern (MID) AF: 0.699 AC: 144 AN: 206

European-Non Finnish (NFE) AF: 0.704 AC: 37055 AN: 52643

Other (OTH) AF: 0.612 AC: 925 AN: 1511

Alfa AF: 0.583 Hom.: 8970

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		0.77
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5906883; hg19: chrX-43526943;